Molecular Mechanisms of Retrovirus Infection

The family of Retroviruses are characterized by their ability to
incorporate viral DNA into a host cell's genome. Most retroviruses
like Rous sarcoma virus (RSV), infect dividing cells during mitosis,
when the chromatin is exposed to the
cytoplasm. Conversely, the genus of Lentiviruses, like the human
immunodeficiency virus (HIV), have evolved in order to infect
non-dividing cells. Since the host cell's chromatin is protected by
the nucleus, the HIV infection process requires coordination between
reverse transcription of viral RNA and nuclear import. Viral RNA is
encased in a shell of the capsid protein CA.

AIDS is caused by the human immunodeficiency virus (HIV). The virus
has the ability to infect non-dividing cells, which means that it
first needs to establish a pathway into the cell and then permeate the
cell's nucleus. For this purpose it enters a cell and recruits cell
factors to assist the orchestration of a complex process leading to
insertion of the viral RNA into the cell's genome. The infection
process involves the capsid surface, a protein shell that encases the
viral genome; we just don't know how this process happens. The capsid
is a natural therapeutical target as ape cells prevent infection by
targeting the capsid. In an experimental-computational collaboration
we have successfully established the atomic-level structure of the HIV
capsid and could characterize the capsid surface properties, capsid
surface processes as well as capsid surface interactions with host
proteins and small molecules.

Originally thought to play a trivial role in the infection process,
the HIV mature capsid is now well established that the viral
capsid fulfills several essential functions.
In particular, capsid involvement in the prevention of
innate sensor triggering, regulation of reverse transcription, and
regulation of the nuclear import pathway is of central importance to
the successful infection of a host cell.

When HIV infects a human cell, it
releases into the interior of the cell its capsid (made of about 1,300
identical so-called CA proteins), a closed, stable container that
protects the viral genetic material (see also June 2013
highlight Elusive
HIV-1 Capsid and August 2015
highlight Anatomy
of a Dormant Killer). Once in the cell ― while avoiding
detection by cellular proteins ― the capsid deceives the cell and
directs the cell machinery to transport it to the nucleus. The
human-cell protein Cyclophilin A (CypA) is thereby exploited to act
against the cell's well being and to assist the HIV infection by
getting the capsid to access the cell nucleus; this results in a
delicate choreography accomplished by escaping anti-viral proteins in
the cell and deceiving transport proteins at the nucleus, all of which
contain a CypA domain that interacts directly with the capsid. Despite
the availability of the crystal structure of the complex of CypA and
CA proteins determined nearly 20 years ago, the mechanism by which
CypA assists the capsid has been unclear due to the lack of
information on CypA in complex with not one CA protein, but the entire
capsid. In collaboration
with experimental groups,
computational biologist have shown in a
recent report
that the effects of CypA on the capsid are not only structural, but
also dynamical. Thus, new therapeutic strategies may be envisioned
through modulation of the dynamics of the capsid by small-molecule
(drug) compounds that inhibit the binding of CypA to the capsid. More
information is available in a
YouTube video.

After a retrovirus is assembled and budded off from the infected host cell,
the virus is in its immature form where the viral proteins
are arranged in a roughly spherical capsid.
These viral proteins, also known as Gag polyproteins,
contain the matrix (MA), capsid (CA) and nucleocapsid (NC) proteins.
Upon maturation by proteolytic cleavage of Gag, immature retroviruses turn into
infectious, mature virions.
For RSV and HIV, one of the early cleavage events involves space peptide (SP),
situated in between CA and NC.
There is currently no consensus on the high resolution structure of SP in its assembled state.
Therefore, obtaining an atomic model of immature retroviral lattice that includes
the SP domain is paramount to provide valuable structural insight.

An all-atom model of an immature RSV lattice was constructed based on a
subnanometer resolution structure of Mason-Pfizer monkey virus (M-PMV)
previously obtained via cryo-electron microscopy (cryo-EM).
Additional Gag components, namely p10 and SP-NC, were incorporated into
the immature lattice model, without which the immature lattice would be unstable.
SP-NC was modeled as a six-helix bundle and was simulated for almost 10 µs
of replica exchange molecular dynamics simulations.
The resulting model of the RSV Gag lattice shows features and dynamics of
the capsid protein with implications for the maturation process.

SP is a drug target of great interest because inhibiting the cleavage of SP-NC
would severely jeopardize the maturation process of the virus.
Preclinical drugs like Bevirimat (BVM) target the SP domain to inhibit the SP-NC
cleavage, however they did not pass the clinical trial.
Having characterized the structure and the dynamics of an assembled SP
would hopefully shed light to the development of next-generation of
maturation inhibitors.

RSV: The homology model of the immature RSV lattice reported in (Structure, 23:1-12, 2015)
is available here for download.

Molecular dynamics trajectory of capsid structure 3J3Y.

In (Nature, 497:643-646, 2013) we report a 64 million atom molecular
dynamics simulation of structure 3J3Y that revealed stability as seen
in a 100 ns trajectory. This claim is corroborated here through
snapshots of the trajectory at 50 ns, 60 ns, ... 100 ns to which we
add for the sake of comparison the pdb entry 3J3Y. The snapshots can
be viewed through VMD.

To open the trajectory simply use VMD to open the PSF file (File ->
New Molecule -> HIVcapsid.pdf), and then add the dcd file (File ->
Load Data Into Molecule -> HIVcapsid.dcd).

The reader can inspect that the simulated structure indeed remains
stable and close to the structure reported in the protein data base.
Further details of the trajectory will be reported in a forthcoming
publication.

In releasing the trajectory data we follow the example of David Shaw
Research who likewise released trajectory data for protein folding,
except that we do not require registration and signing of a license.
The latter generosity is simply dictated by our lack of legal support,
but we expect that the use of the trajectories is properly
acknowledged through explicit reference of use of the trajectories and
of Nature, 497:643-646, 2013.